Unknown

Dataset Information

0

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints.


ABSTRACT: Experimental detection of RNA splicing branchpoints is difficult. To date, high-confidence experimental annotations exist for 18% of 3' splice sites in the human genome. We develop a deep-learning-based branchpoint predictor, LaBranchoR, which predicts a correct branchpoint for at least 75% of 3' splice sites genome-wide. Detailed analysis of cases in which our predicted branchpoint deviates from experimental data suggests a correct branchpoint is predicted in over 90% of cases. We use our predicted branchpoints to identify a novel sequence element upstream of branchpoints consistent with extended U2 snRNA base-pairing, show an association between weak branchpoints and alternative splicing, and explore the effects of genetic variants on branchpoints. We provide genome-wide branchpoint annotations and in silico mutagenesis scores at http://bejerano.stanford.edu/labranchor.

SUBMITTER: Paggi JM 

PROVIDER: S-EPMC6239175 | biostudies-literature |

REPOSITORIES: biostudies-literature

Similar Datasets

2022-10-12 | GSE214998 | GEO
| S-EPMC5449545 | biostudies-literature
| S-EPMC5759031 | biostudies-literature
| S-EPMC7682815 | biostudies-literature
| S-EPMC8876403 | biostudies-literature
| S-EPMC7868753 | biostudies-literature
| S-EPMC9200721 | biostudies-literature
| S-EPMC7521708 | biostudies-literature
| S-EPMC7803766 | biostudies-literature
2024-02-03 | GSE254493 | GEO